SOX9 recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. The isolated cDNA corresponded to 3.9 kb of the transcript, but Northern blot analysis detected a 4.5-kb transcript in adult testes, adult heart, and fetal brain. The SOX9 protein HMG box domain at amino acids 104-182 showed 71% similarity with the SRY HMG box, and the C-terminal third of the protein has a proline- and glutamine-rich region similar to activation domains present in some transcription factors. The genomic arrangement of SOX9 is such that the 5-prime end is oriented toward the centromere of chromosome 17 and closest to the breakpoint. It is possible that 1 or more exons are present 5-prime to the known exons and that these are disrupted by the translocation.